ライフサイエンスコーパス: minor groove

1 erting a beta sheet 'wing' into the adjacent minor groove.

2 binding, likely through interaction with the minor groove.

3 cooperative binding of Hoechst 33258 at the minor groove.

4 ly recognize the G-NH that projects into the minor groove.

5 DNA sequences to allow narrowing of the DNA minor groove.

6 ling that is due to alkylation of DNA in the minor groove.

7 that binds to AT base pair sites in the DNA minor groove.

8 s, accompanied by contacts with the flanking minor groove.

9 upon binding a specific sequence through the minor groove.

10 mparable with the canonical width of the DNA minor groove.

11 mall molecules in the AT region of the B-DNA minor groove.

12 e by DNase I closely tracks the width of the minor groove.

13 ater-mediated hydrogen bonds with p53 at the minor groove.

14 TG/CA step and shows intercalation from the minor groove.

15 domain (dsRBD) helix alpha1 to the tetraloop minor groove.

16 able to methylation-induced narrowing of the minor groove.

17 lted in a kinked DNA duplex with an enlarged minor groove.

18 resulting in a straighter DNA with narrower minor groove.

19 he modified base from the sterically crowded minor groove.

20 DNA, including the spine of hydration in the minor groove.

21 m the intrusion of IL molecules into the DNA minor groove.

22 heir Watson-Crick edges displaced toward the minor groove.

23 ding of the relatively straight DNA into the minor groove.

24 y rings form pi-stacked complexes within the minor groove.

25 g that the N-terminal extension binds in the minor groove.

26 he major groove from those that occur in the minor groove.

27 tates DNA bending through compression of the minor groove.

28 ds K(26), W(27), K(28), and K(29) are in the minor groove.

29 long the phosphate backbone and bridging the minor groove.

30 e induced by cyclic polyamide binding in the minor groove.

31 inal 'arms' that appear to 'compete' for the minor groove.

32 modated by severe compression of the central minor groove.

33 n as a reference A5 tract, that is, into the minor groove.

34 e, and the wing interacted with the adjacent minor groove.

35 r, and occurs toward either the major or the minor groove.

36 ct has a high tendency of bending toward the minor groove.

37 ntered preferentially on an exposed major or minor groove.

38 , and of ~1.5 kcal/mol for sliding along the minor groove.

39 sults from water fixed by the AT pair in the minor groove.

40 lization of Li(+) ions in the narrow A-tract minor groove.

41 We show that CbpA interacts with the DNA minor groove.

42 ter-bridged hydrogen-bonding networks in the minor groove.

43 not strongly discriminate between major and minor grooves.

44 on of the damaged base through the major and minor grooves.

45 t roles in differentiating the TTAA and AATT minor grooves.

46 nchoring" lysines and arginines into the DNA minor grooves.

47 r findings that in the case of the family of minor groove 10S (+)-trans-anti-B[a]P-N(2)-dG lesions, f

48 Arg42 are predicted to be located in the DNA minor groove 5' to the modified cytosine.

49 xic interstrand cross-links (ICLs) and bulky minor groove adducts normally recognized by Fanconi anem

50 e that there is complexity in the binding of minor groove agents to a single site.

51 constructed two duplexes containing the same minor groove-aligned 10S (+)-trans-anti-B[a]P-N(2)-dG (G

52 of the DB[a,l]P-dG lesion in contrast to the minor groove alignment of the B[a]P-dG adduct, and the i

53 oxia-selective metabolism to form potent DNA minor groove-alkylating agents.

54 d protein) and binding modes (intercalation, minor groove, allosteric switch).

55 Interactions with the guide-target minor groove allow Ago2 to interrogate target RNAs in a

56 nteractions between conserved Arg-86 and the minor groove and a large network of non-base-specific co

57 However, P22R NTD induces a narrow minor groove and a spine of hydration to 5'-ACGT-3'.

58 Usually the B' state, with a narrow minor groove and a spine of hydration, is reserved for A

59 distamycin-type ligands of DNA that bind the minor groove and are capable of sequence selective recog

60 g the third zinc finger bind in the opposing minor groove and are required for high-affinity binding.

61 Then Fis further compresses the minor groove and bends the DNA to generate the bound str

62 The DNA is contacted from the minor groove and bent towards the major groove.

63 can sense the structural changes of the DNA minor groove and can be considered a "minor groove senso

64 ethodology, DNAphi, for predicting EP in the minor groove and confirmed the direct role of EP in prot

65 their Watson-Crick edges rotated toward the minor groove and exhibit only modest flexibility.

66 LI1-DNA structure suggest that MTM binds the minor groove and perturbs FLI1 bound nearby in the major

67 nition mechanisms involving the shape of the minor groove and sequence-dependent induced fits over ad

68 ighboring thymine bases in Ox-TGGA crowd the minor groove and sterically hinder the motion of the dia

69 3-MeA protrudes into the DNA minor groove and strongly blocks synthesis by replicativ

70 nd that the 2'-Se modification points to the minor groove and that the modified and native structures

71 BD utilizes the wing and helix-B to bind the minor groove and the major groove of the MCB-DNA whilst

72 part, with one linker segment located in the minor groove and the other in the major groove consisten

73 The protein/RNA interface involves two minor grooves and has no sequence-specific contacts, wit

74 e measured for removing the ligands from the minor groove, and of ~1.5 kcal/mol for sliding along the

75 o the overall fit of the molecule in the DNA minor groove, and potential specific contacts with funct

76 , with the IQ H4a and CH3 protons facing the minor groove, and the IQ H7a, H8a and H9a protons facing

77 Treatment with the minor groove- and GC-specific chemical chromomycin A(3)

78 ion that corresponds to accessibility of the minor groove as DNA winds around the nucleosome--we deve

79 ethylene linker is primarily situated in the minor groove as indicated by an increase in fluorescence

80 nucleosomes matching the exposure of the DNA minor groove as it wraps around histones.

81 g mode in importin alpha1 that uses only the minor groove as the exclusive site for nuclear import of

82 he complexes were manually inserted into the minor groove as the starting point of the simulations.

83 e uniquely presented by the RPo: the splayed minor groove at the double-stranded/single-stranded DNA

84 curvature, not cation binding in the A-tract minor groove, because identical free solution mobilities

85 to be a free energy offset between major and minor groove bending.

86 NP residues 214 and 217 localize at the minor groove between the two opposite-polarity NP helica

87 new set of primers and corresponding TaqMan Minor Groove Binder (MGB) probes were designed to target

88 rmational changes of DNA upon binding of the minor groove binder netropsin.

89 rphase chromosomes were labeled with the DNA minor groove binder, DAPI, followed by measurement and i

90 hence suggesting the possibility of being a minor groove binder.

91 , and we demonstrated that intercalators and minor groove binders affect the conformation of the DNA

92 diaromatic guanidines with potential as DNA minor groove binders and antiprotozoal activity.

93 ium aromatic derivatives (4a-g) as potential minor groove binders and cytotoxic agents.

94 ranscription elongation by sequence-specific minor groove binders may present opportunities to target

95 otozoal activity of most of these aminoalkyl minor groove binders was evaluated in vitro against Tryp

96 pounds, derived from existing classes of DNA minor groove binders, were designed, synthesized, and ev

97 de linked diaromatic dications as potent DNA minor groove binders.

98 re we investigate the mechanism of how these minor-groove binders affect pol II transcription elongat

99 A system of specific primers and a Minor Groove Binding (MGB) TaqMan probe based on sequenc

100 For this purpose, specific primers and a minor groove binding (MGB) TaqMan probe were designed to

101 oup of mahanine for its cytotoxicity and its minor groove binding ability with DNA.

102 Many minor groove binding agents selectivity recognize AT ove

103 Structural results with minor groove binding agents, such as netropsin, have pro

104 pecific, highly efficient, dynamic nature of minor groove binding agents.

105 ugh interaction modes like intercalation and minor groove binding already have been identified, assoc

106 Although it has been difficult to get minor groove binding at TTAA, DB293, a phenyl-furan-benz

107 l for the conformational flexibility and DNA minor groove binding by Mor.

108 ect dAMPcPP analog but with formation of the minor groove binding conformer.

109 The minor groove binding hairpin 3 inhibits DNA methyltransf

110 We report that a DNA minor groove binding hairpin pyrrole-imidazole (Py-Im) p

111 of six similar compounds has three different minor groove binding modes with the target sequences.

112 d the optimal targeting of sequence-specific minor groove binding molecules, an essential underpinnin

113 Considering the strong DNA minor groove binding observed for our previous series of

114 To assess the utility of minor groove binding oligomers for CpG recognition, we s

115 gonucleotides, peptide nucleic acids (PNAs), minor groove binding polyamides, and--more recently--eng

116 In contrast to the minor groove binding seen for Isw1 and predicted for Chd

117 ion of the complex, as well as demonstrating minor groove binding specificity.

118 nformation, including an outward rotation of minor groove binding wings, an inward movement of helix-

119 The DNA aggregation and minor groove binding with redox molecule cause a signifi

120 s could be assigned to bis-intercalation and minor groove binding, respectively, DRAQ5 exhibited both

121 DNA by intercalation, whereas DAPI exhibits minor groove binding.

122 PBDs) are a family of sequence-selective DNA minor-groove binding agents that form a covalent aminal

123 Two short minor-groove binding fluorescent probes targeting the po

124 Unlike a proposed minor-groove binding model based on methylation interfer

125 DNA binding, discrete from intercalation and minor-groove binding.

126 sequence-specific ETS-DNA binding, using the minor groove-binding distamycin as a model compound.

127 ucturally related and structurally unrelated minor groove-binding ligands.

128 yl sulfonate leaving group and a neutral DNA minor groove-binding side chain, displayed hypoxic cytot

129 l discrimination of nucleic acid duplexes by minor-groove-binding ligands is presented.

130 s seen within the interfaces between DNA and minor-groove-binding proteins.

131 showed that (+)-anti-BPDE primarily adopts a minor groove bound orientation within the oligomers whil

132 s on an AT-sequence, we show that the ICD of minor-groove-bound 4',6-diamidino-2-phenylindole (DAPI)

133 All of the proteins bound in the minor groove, bridging DNA molecules, presumably because

134 ated that the ligands fit tightly within the minor groove, causing little distortion of the helix.

135 t the complex binds to the mismatch from the minor groove, characteristic of metalloinsertion.

136 ediated phosphate neutralization facilitates minor groove compression and is particularly important f

137 exo(-) complex adopts a mix of the major and minor groove conformers with minimal effect upon the add

138 y quantitative DNA footprinting revealed new minor groove contacts and changes in the core consensus

139 gest past ICLs induced by the non-distorting minor groove cross-linking agent SJG-136, albeit with SN

140 dimers are synthetic sequence-selective DNA minor-groove cross-linking agents that possess two elect

141 The fraction of cations in the minor groove decreases for the larger Sr(2+) ions and be

142 Gh by allowing G568 to move in the major-to-minor groove direction of the P/T.

143 ohydrate-based ligands to study carbohydrate-minor groove DNA interactions.

144 to induce a syn-8-oxoG conformation without minor groove DNA polymerase interactions that influence

145 The promiscuity inherent to minor groove DNA recognition rationalizes the observatio

146 Here, we report the identification of the minor groove DNA-binding factor high mobility group AT-h

147 These results show how RNA Pol II copes with minor-groove DNA alkylation and establishes a mechanism

148 Minor-groove DNA binding by the HMG box results in subst

149 the misincorporation of dCMP opposite these minor-groove DNA lesions, whereas only Pol V was indispe

150 salt concentration, [M(+)], for 33 cationic minor groove drugs binding to AT-rich DNA sequences is s

151 and shape readout through recognition of the minor-groove electrostatic potential by lysine.

152 o bind to duplex DNA, apparently requiring a minor groove environment for covalent bond formation bet

153 some water molecules confined in the narrow minor groove exhibit very slow dynamics.

154 mine moieties can bind covalently in the DNA minor groove, forming an interstrand cross-link.

155 drial DNA polymerase but, in the case of the minor groove gamma-HOPdG adduct, at the cost of unpreced

156 gated the ability of pol gamma to bypass the minor groove gamma-HOPdG and major groove gamma-HOPdA ad

157 We shed light on the way the minor groove geometry, defined mainly by the DNA sequenc

158 or groove (base readout), proteins recognize minor-groove geometry using positively charged amino aci

159 and AAATT sequences, which have more narrow minor grooves, have smaller mobility changes on binding

160 ecreased 10(2)-10(3)-fold even when only one minor groove HB interaction was missing.

161 ch makes 3DA an optimal analogue for probing minor groove HB interactions between a DNA polymerase an

162 The minor groove HB interactions between position n - 2 of t

163 , we decided to evaluate the contribution of minor groove HB interactions with family B pols.

164 pt W-C H-bonding, stacking interactions, and minor groove hydrations to some extent at the modified s

165 Minor groove hydrogen bonding (HB) interactions between

166 syn-conformation of 8-oxoG is stabilized by minor groove hydrogen bonding between the side chain of

167 B[a]P ring system to produce a more enlarged minor groove in CG*C-II than in CG*C-I, as well as a loc

168 s a negative polarization at the edge of the minor groove in the absence of a hydrophilic 2'-substitu

169 ly excluded from the vicinity of the A-tract minor groove, increasing the effective net charge of the

170 ll-based transcription studies indicate that minor groove interaction by Arg349 located in the Ets do

171 ndergoes electrostatic and sequence-specific minor groove interactions with DNA, is used as a prototy

172 inantly by a single residue, R517, which has minor groove interactions with the DNA template.

173 e G and additional modifications for general minor groove interactions.

174 igm that does not fit the classical model of minor groove interactions.

175 ticancer agents that form DNA adducts in the minor groove interfere with DNA replication and transcri

176 base pair step is kinked or a region of the minor groove is narrow).

177 Water in the minor groove is, thus, orchestrated by the arrangement o

178 served histidine that interacts with the DNA minor groove, is disordered in apo IRF-3 but is ordered

179 ence d(CGCGAATTCGCG)(2) complexed with three minor-groove ligands are reported.

180 ngs emphasize the critical nature of the DNA minor groove microstructure for sequence-specific recogn

181 r, the factors that govern the propensity of minor groove narrowing are not completely understood.

182 se pairs of the DNA helix that lead to local minor-groove narrowing and enhanced electrostatic intera

183 Previous studies showed that the minor-groove O(2)-alkylated thymidine (O(2)-alkyldT) les

184 ro=chromomycin A3) binds specifically to the minor groove of (CCG)n repeats in duplex DNA, with uniqu

185 ions of the native loop structure within the minor groove of adjacent helical regions.

186 c amino acid side chains can insert into the minor groove of an Scr-specific DNA-binding site.

187 ing protein that specifically recognizes the minor groove of AT-rich DNA sequences.

188 ed to a tight fit of the molecule inside the minor groove of AT-rich DNA which induces geometrical re

189 We showed that diamidines target the minor groove of AT-rich sequences on one or both sides o

190 ves prepared have the ability to bind to the minor groove of certain DNA sequences and intercalate to

191 imilar mechanism involving contacts with the minor groove of DNA and oligomerization.

192 ized class cannot be accommodated within the minor groove of DNA due to a change in the shape of the

193 and TMA are preferentially localized in the minor groove of DNA duplexes at A.T base pairs and these

194 yrrole-imidazole (PI) polyamides bind to the minor groove of DNA in a sequence-specific manner withou

195 yrrole-imidazole polyamides that bind to the minor groove of DNA in a sequence-specific manner withou

196 ected by a kink, interacts with the adjacent minor groove of DNA in the models.

197 Arg5 interacts with thymine in the minor groove of DNA through hydrogen bonding and electro

198 tat92E indicates that R(442) may contact the minor groove of DNA via invariant TC bases in the consen

199 ntaining side chains designed to bind in the minor groove of DNA while spanning a wide range of base

200 ole-imidazole (Py-Im) polyamides bind to the minor groove of DNA with programmable sequence specifici

201 PDB-ID: 5LIT) shows that the drug covers the minor groove of DNA, displaces bound water and interacts

202 own for their specific interactions with the minor groove of DNA.

203 Daunomycin initially binds in the minor groove of DNA.

204 he proteins make important contacts with the minor groove of DNA.

205 e derivatives, which preferentially bind the minor groove of double-stranded DNA, inhibit vaccinia vi

206 ese ligands bind covalently edge-on into the minor groove of double-stranded DNA.

207 ffect of the alkyl group projecting into the minor groove of double-stranded RNA preventing off-targe

208 in unusual base-specific recognition in the minor groove of dsRNA are conserved between NF90 and ADA

209 ith antiparasitic properties that target the minor groove of kinetoplast DNA.

210 lly recognizes a single G*C base pair in the minor groove of mixed base pair sequences of the type AA

211 The proximity of the AP residues across the minor groove of the -3 duplex and across the major groov

212 within the IIB1 class and interacts with the minor groove of the catalytic domain V.

213 s symmetrically and perpendicularly from the minor groove of the d(CCGGTACCGG)(2) duplex at the centr

214 the DNA-bound Rb(+) ions penetrate into the minor groove of the DNA and half adsorb on the DNA backb

215 to interact with the N3 and O2 atoms in the minor groove of the DNA duplex.

216 two tyrosine residues, which insert into the minor groove of the DNA duplex.

217 ur studies show that fdG is tolerated at the minor groove of the DNA to a better extent compared with

218 uggested that AlkA actively interrogates the minor groove of the DNA while probing for the presence o

219 tage the protein can bind both the major and minor groove of the DNA, but uses different features to

220 ese two DNA-binding domains bind to the same minor groove of the DNA.

221 so contacts sequences of the A-site from the minor groove of the DNA.

222 domain alpha helix that is positioned in the minor groove of the double-stranded RNA product and lysi

223 h the prediction that Mor interacts with the minor groove of the GC-rich spacer in the Mor binding si

224 n to interact with the DNA strand, cross the minor groove of the helix, and then form Van der Waals c

225 ermore, we identify functional groups in the minor groove of the non-contacted bases as the essential

226 G568 the flexibility to move deeper into the minor groove of the P/T to accommodate, and stabilize, s

227 adopt an extended conformation spanning the minor grooves of helices 89 and 91 of the 23S rRNA and i

228 mong all viral particles, with the major and minor grooves of RNA helices clearly visible.

229 s to interact with the consecutive major and minor grooves of the GTTAG signature sequence.

230 ions with functional groups in the major and minor grooves of the target DNA.

231 s the major groove flanking the nick and the minor groove on the 3'-OH side of the nick.

232 in which the B[a]P rings reside in the B-DNA minor groove on the 3'-side of the modifed deoxyguanosin

233 The OB domain engages the DNA minor groove on the face of the duplex behind the nick,

234 alpha-helix that interacts with a downstream minor groove on the same face of the DNA.

235 aused by differences in helix untwisting and minor groove opening that are derived from the differenc

236 base sequence-dependent local untwisting and minor groove opening together with weaker stacking inter

237 to the free energy of deforming (bending and minor groove opening) the drug-DNA molecule during HMGB1

238 cking interactions, and cause untwisting and minor groove opening.

239 ns of protein around DNA including major and minor groove orientations.

240 The minor groove pathway and free energy barrier (6-7 kcal/m

241 dimer complex to match the curvature of the minor groove play important roles in differentiating the

242 The presence of a minor groove-positioned guanine amino group, the Watson-

243 e highest-affinity interactions occur in the minor groove, primarily through a deeply penetrating arg

244 uanosine that contain cyclopentyl and propyl minor-groove projections.

245 wedge-shaped loop from Rpb2 that engages its minor groove, providing part of the structural framework

246 in which the 5-methyl group points into the minor groove, rather than the major groove as in a norma

247 on properties and different requirements for minor groove recognition.

248 istinctive modes of interactions between the minor groove residues.

249 ly demanding 8-alkoxy groups in the major or minor groove, respectively, of duplex RNA.

250 he DNA minor groove and can be considered a "minor groove sensor." Prolonged interference of transcri

251 appropriate radius of curvature to match the minor groove shape and represents a new paradigm that do

252 G PAM is recognized in duplex form, from the minor groove side, by three structural features in the C

253 thus their pendant methyl groups are on the minor groove side.

254 methyladenine (3-dMeA), which blocks the DNA minor groove similarly to 3-MeA.

255 ort formation of a highly ordered and stable minor groove solvation network are a key determinant of

256 is achieved by molecular recognition through minor groove spanning and backbone tracking of the phosp

257 y suggest that DNA condensation is driven by minor-groove spanning.

258 sites, creating an array of complexes in the minor groove stabilized by stacking interactions between

259 The RNA kinks by an association of the two minor grooves, stabilized by the formation of a number o

260 d PBD/DNA adducts despite a complete loss of minor groove structure was further confirmed by CD spect

261 l effects of heterocyclic diamidines on four minor groove target sequences: AAAAA, TTTAA, AAATT and A

262 is structural information, we designed a DNA minor groove-targeted polyamide that inhibits NES with l

263 tational orientation of CpGs such that their minor grooves tended to face toward the histones in the

264 The interaction between the minor groove tetrads and the nearby C:C(+) base pairs af

265 protonated C:C(+) base pairs, flanked by two minor groove tetrads resulting from the association of G

266 tin binding through interaction with the DNA minor groove that flanks PU.1-binding motifs.

267 ies of the local DNA shape: the width of the minor groove, the relative orientations of adjacent base

268 approach using small molecules to target the minor groove to control expression by an allosteric mech

269 proteins prefer DNA sequences with distinct minor groove topographies.

270 elects DNA targets with intrinsically narrow minor grooves using the separation between helix-turn-he

271 The width of the DNA minor groove varies with sequence and can be a major det

272 conserved CarD Trp residue that serves as a minor groove wedge, preventing collapse of the transcrip

273 al heterogeneity is especially strong in the minor groove, where groove width fluctuations occur on t

274 antimalarial activity by binding to the DNA minor groove whereas other sets of compounds could exert

275 The wings insert into the flanking minor grooves, whereby residue Arg87, buttressed by Asp8

276 of many exposed reactive sites is a wide DNA minor groove, which allows penetration of a key active s

277 pecifier Sequence bases to rotate toward the minor groove, which increases accessibility for pairing

278 were generally larger for bending toward the minor groove, which is thought to originate from differe

279 ery via placement of the alkoxy group in the minor groove, while maintaining significant RNAi efficac

280 PG-specific manner and demarcated by general minor groove widening.

281 oundary of the A/T and G/C regions where the minor groove widens.

282 A sequence that is consistent with decreased minor groove width and bending of the relatively straigh

283 pe features, Propeller twist, Helical twist, Minor groove width and Roll.

284 Because minor groove width is highly governed by 3-base periodic

285 s-DNA complex narrows to about half the mean minor groove width of canonical B-form DNA to fit onto t

286 pair and six inter-base pair parameters and minor groove width, is available in our R/Bioconductor p

287 for DNA shape annotations (GBshape) provides minor groove width, propeller twist, roll, helix twist a

288 redicts multiple structural features of DNA (minor groove width, roll, propeller twist and helix twis

289 tive data for DNA structural features (i.e., minor groove width, roll, propeller twist and helix twis

290 f poly(A) sequences associated with narrowed minor groove width.

291 ape readout involves the correlation between minor-groove width and electrostatic potential (EP).

292 ophysical effect directly, rather than using minor-groove width as an indirect measure for shape read

293 s are sufficient to reproduce the changes in minor groove widths and recreate the curved Fis-bound DN

294 N(2)-dG lesions, flexible bends and enlarged minor groove widths constitute NER recognition signals,

295 nstrate that sequence-dependent narrowing of minor groove widths is modulated almost entirely by the

296 step parameters, helix parameters, and major/minor groove widths to examine how the presence of multi

297 he primary molecular determinant controlling minor groove widths.

298 y, remove or add an amino group from the DNA minor groove, with corresponding changes in hydrogen-bon

299 For example, the minor groove within the center of the Fis-DNA complex na

300 zag spine pattern of hydrogen bonding in the minor groove without manual intervention.